Results Report
Metadata:
The report shows the results of the sample: PXD003013_Cowpox_BR
Piechart showing the number of PSMs found for the first three
searches.
Host Filtering:
MultiStageSearch filtered 2069 host spectra
Reference Database Search:
The left plot shows the weighting of candidate taxa at species level,
which build the basis for the next search steps.
The right plot
shows the confidence distribution of the found
PSMs.
Fetching of Data:
Table showing the fetched genomes with according metadata such as Taxon-ID or strain name:
The log file for the fetchData step can be found here:
/storage/mi/pipaj97/MA/MA_MSS/results/logs/PXD003013_Cowpox_BR/FetchData/fetchStrainGenomes/stdout.log
It can happen that some sequence records are imediatly removed by
the step, due to problems for the record. (i.e. no sequence for the
sequence record is found)
TaxIDs used: [10243]
Querying for TaxId:
10243
1/max409; Sequence ID: 1551911402, Sequence Lenght:
229131
2/max409; Sequence ID: 1551910651, Sequence Lenght:
228534
3/max409; Sequence ID: 1551911778, Sequence Lenght:
228530
4/max409; Sequence ID: 1551909550, Sequence Lenght:
228369
5/max409; Sequence ID: 1551909736, Sequence Lenght:
228367
6/max409; Sequence ID: 1210074670, Sequence Lenght:
228276
7/max409; Sequence ID: 90660233, Sequence Lenght:
228250
8/max409; Sequence ID: 925059618, Sequence Lenght:
228162
9/max409; Sequence ID: 925059915, Sequence Lenght:
227639
10/max409; Sequence ID: 325557951, Sequence Lenght:
226424
11/max409; Sequence ID: 2295693327, Sequence Lenght:
226090
12/max409; Sequence ID: 1193117912, Sequence Lenght:
225395
13/max409; Sequence ID: 1193117288, Sequence Lenght:
225263
14/max409; Sequence ID: 325558165, Sequence Lenght:
225136
15/max409; Sequence ID: 1193117086, Sequence Lenght:
224952
16/max409; Sequence ID: 1193117711, Sequence Lenght:
224936
17/max409; Sequence ID: 1210075533, Sequence Lenght:
224837
18/max409; Sequence ID: 1551910279, Sequence Lenght:
224665
19/max409; Sequence ID: 325558595, Sequence Lenght:
224595
20/max409; Sequence ID: 30795158, Sequence Lenght:
224499
21/max409; Sequence ID: 30844336, Sequence Lenght:
224499
22/max409; Sequence ID: 1735180497, Sequence Lenght:
224139
23/max409; Sequence ID: 1551911021, Sequence Lenght:
223850
24/max409; Sequence ID: 1388153167, Sequence Lenght:
223759
25/max409; Sequence ID: 1375958567, Sequence Lenght:
223701
26/max409; Sequence ID: 1210076101, Sequence Lenght:
223681
27/max409; Sequence ID: 30519405, Sequence Lenght:
223666
28/max409; Sequence ID: 1147161605, Sequence Lenght:
223595
29/max409; Sequence ID: 1210074964, Sequence Lenght:
223583
30/max409; Sequence ID: 1551911587, Sequence Lenght:
223508
31/max409; Sequence ID: 1210073544, Sequence Lenght:
223357
32/max409; Sequence ID: 1551910835, Sequence Lenght:
223225
33/max409; Sequence ID: 1551911212, Sequence Lenght:
223150
34/max409; Sequence ID: 1210076384, Sequence Lenght:
223088
35/max409; Sequence ID: 325558812, Sequence Lenght:
222555
36/max409; Sequence ID: 1210077799, Sequence Lenght:
222376
37/max409; Sequence ID: 1210077235, Sequence Lenght:
222189
38/max409; Sequence ID: 2325507948, Sequence Lenght:
222178
39/max409; Sequence ID: 1210076669, Sequence Lenght:
222113
40/max409; Sequence ID: 325557737, Sequence Lenght:
222105
41/max409; Sequence ID: 1210076951, Sequence Lenght:
222104
42/max409; Sequence ID: 1048493253, Sequence Lenght:
222069
43/max409; Sequence ID: 1375958007, Sequence Lenght:
222062
44/max409; Sequence ID: 1210075819, Sequence Lenght:
222058
45/max409; Sequence ID: 1375958287, Sequence Lenght:
221930
46/max409; Sequence ID: 2325507732, Sequence Lenght:
221926
47/max409; Sequence ID: 1210073825, Sequence Lenght:
221816
48/max409; Sequence ID: 325559238, Sequence Lenght:
221530
49/max409; Sequence ID: 325514012, Sequence Lenght:
221512
50/max409; Sequence ID: 2325508166, Sequence Lenght:
221334
51/max409; Sequence ID: 554574583, Sequence Lenght:
221194
52/max409; Sequence ID: 1375958850, Sequence Lenght:
221171
53/max409; Sequence ID: 554574102, Sequence Lenght:
221153
54/max409; Sequence ID: 554575718, Sequence Lenght:
221071
55/max409; Sequence ID: 1375957698, Sequence Lenght:
220997
56/max409; Sequence ID: 2325507514, Sequence Lenght:
220981
57/max409; Sequence ID: 1210074112, Sequence Lenght:
220975
58/max409; Sequence ID: 1210074393, Sequence Lenght:
220958
59/max409; Sequence ID: 325559026, Sequence Lenght:
220915
60/max409; Sequence ID: 1862966302, Sequence Lenght:
220822
61/max409; Sequence ID: 2325507296, Sequence Lenght:
220808
62/max409; Sequence ID: 1210075252, Sequence Lenght:
220621
63/max409; Sequence ID: 325558381, Sequence Lenght:
220280
64/max409; Sequence ID: 2233348798, Sequence Lenght:
220276
65/max409; Sequence ID: 1679574850, Sequence Lenght:
219385
66/max409; Sequence ID: 1551910101, Sequence Lenght:
218251
67/max409; Sequence ID: 1193118312, Sequence Lenght:
217955
68/max409; Sequence ID: 554572228, Sequence Lenght:
217406
69/max409; Sequence ID: 554572927, Sequence Lenght:
216813
70/max409; Sequence ID: 1735181190, Sequence Lenght:
216799
71/max409; Sequence ID: 554572692, Sequence Lenght:
216415
72/max409; Sequence ID: 554571521, Sequence Lenght:
216357
73/max409; Sequence ID: 554574815, Sequence Lenght:
216271
74/max409; Sequence ID: 554571749, Sequence Lenght:
215715
75/max409; Sequence ID: 1551909371, Sequence Lenght:
214880
76/max409; Sequence ID: 1169132791, Sequence Lenght:
214707
77/max409; Sequence ID: 554575259, Sequence Lenght:
214048
78/max409; Sequence ID: 1551909922, Sequence Lenght:
213972
79/max409; Sequence ID: 1551910466, Sequence Lenght:
213486
80/max409; Sequence ID: 554571289, Sequence Lenght:
213325
81/max409; Sequence ID: 554571985, Sequence Lenght:
213043
82/max409; Sequence ID: 1243284019, Sequence Lenght:
212910
83/max409; Sequence ID: 554573167, Sequence Lenght:
212909
84/max409; Sequence ID: 554573638, Sequence Lenght:
212814
85/max409; Sequence ID: 554576192, Sequence Lenght:
212773
86/max409; Sequence ID: 554575962, Sequence Lenght:
209262
87/max409; Sequence ID: 554574344, Sequence Lenght:
208980
88/max409; Sequence ID: 1243284458, Sequence Lenght:
204321
89/max409; Sequence ID: 1243283804, Sequence Lenght:
204218
90/max409; Sequence ID: 1243284674, Sequence Lenght:
204015
91/max409; Sequence ID: 1243284243, Sequence Lenght:
203925
92/max409; Sequence ID: 554575494, Sequence Lenght:
201217
93/max409; Sequence ID: 554572464, Sequence Lenght:
200835
94/max409; Sequence ID: 554573866, Sequence Lenght:
200528
95/max409; Sequence ID: 554573411, Sequence Lenght:
197388
96/max409; Sequence ID: 554575035, Sequence Lenght:
197324
97/max409; Sequence ID: 1193117600, Sequence Lenght:
196768
98/max409; Sequence ID: 1193117490, Sequence Lenght:
196570
99/max409; Sequence ID: 41351800, Sequence Lenght:
9450
Sequence length difference exceeds threshold, query ends
here!
Only the 98 longest are used. All others are below the sequence
length difference threshold!
Dropped 0 genomes. They had neither
strain nor isolate information!
Covid Mode:
Activation of the Covid Mode: False
Preparation of proteogenomic Database:
Filtering of duplicate Proteomes:
Similarity of ORFs of ON549927.1 and AF482758.2 =
0.9879488440727988
Similarity exceeds threshold of 98.0%!
Removing
ORFs for Genbank accession ON549927.1!
Removed 4066
ORFs.
Similarity of ORFs of ON549927.1 and NC_003663.2 =
0.9879488440727988
Similarity exceeds threshold of 98.0%!
Removing
ORFs for Genbank accession ON549927.1!
Removed 0
ORFs.
Similarity of ORFs of AF482758.2 and NC_003663.2 =
1.0
Similarity exceeds threshold of 98.0%!
Removing ORFs for
Genbank accession NC_003663.2!
Removed 4037 ORFs.
Heatmap showing the pairwise similarity of the top scoring
proteomes.
Clustering of Open Reading Frames:
Number of sequences: 743204
Number of unique sequences:
97526
Proteogenomic Database Search:
Table showing the scores for the top scoring Taxon-IDs of the
proteogenomic database search
Taxon-ID with the highest count of PSMs: 5000019
Taxon-ID with
the highest confidence scoring: 5000019
Taxon-ID with the highest
weight: 5000019
Taxon-ID with the highest proteome length scoring:
5000019
The left plot shows the counts for the taxa with the highest amounts
of PSMs.
The right plot shows the weighting of the strain taxa with
the highest
weights.
The
left plot shows the strain taxa with the highest confidence scoring.
The right plot shows the strain taxa with the highest
proteome_length_scoring.
The
left plot shows the strain taxa with the highest mean confidences for
the PSMs.
The right plot shows the distribution of the confidence of
PSMs in this search
step.
Top-Scoring Proteogenomic Database Search
Clustering of Open Reading Frames:
Number of sequences: 232674
Number of unique sequences:
52192
Table showing the scores for the top scoring Taxon-IDs of the
top-scoring proteogenomic database search
Taxon-ID with the highest count of PSMs: 5000019
Taxon-ID with
the highest confidence scoring: 5000019
Taxon-ID with the highest
weight: 5000019
Taxon-ID with the highest proteome length scoring:
5000019
The left plot shows the counts for the taxa with the highest amounts
of PSMs.
The right plot shows the weighting of the strain taxa with
the highest
weights.
The
left plot shows the strain taxa with the highest confidence scoring.
The right plot shows the strain taxa with the highest
proteome_length_scoring.
The
left plot shows the strain taxa with the highest mean confidences for
the PSMs.
The right plot shows the distribution of the confidence of
PSMs in this search
step.
Heatmap showing the pairwise similarities of identified peptides.
Database Suitability
Phylogeny
